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Charge Transport in DNA - Insights from Simulations
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DNAUnderExperimentalConditions Table4.7: Force at which the overstretching transition as well as strand separation (melting) occurred. Data from simulations of fully hydrated systems (with two different loading rates) as well as for the systems Dry1, Dry2 and Dry1 with a decreased number of sodium ions. All figures in pN; ‘—’ denotes cases where no clear transition was observed. a The loading rate was 50 pN/ns for A5, A9, G5 and G9 while it was 83 pN/ns for A13 and G13. transition fullyhydrated Dry1 Dry2 Dry1with1/2 ions 50/83pN/nsa 10pN/ns A5 overstretchingat 187 142 288 — 184 separationat 508 458 901 941 860 A9 overstretchingat 199 154 361 — — separationat 746 678 1229 1109 946 A13 overstretchingat 293 173 395 580 335 separationat 1014 708 1365 1331 1674 G5 overstretchingat 172 171 301 309 121 separationat 713 704 932 1112 864 G9 overstretchingat 421 231 432 788 — separationat — 1001 1444 1451 895 G13 overstretchingat 397 314 412 551 298 separationat 1431 1332 1958 1164 1761 The significance of counterions present in the solvent formaintaining thedouble- strandedstructureofDNAwasseen in the freesimulationsalready. Following this line, the stretchingofmicrohydrateddouble-strandedDNAwas investigatedwith a smallernumberof counterions thanrequired toneutralize thenegative chargeof DNAbackbone (see the abovediscussionof such anoccurrence). Performedwere two further simulations for eachDNAoligomer studied: 1. with1/10of thebulknumberofwatermolecules (Dry1) and1/2of thenum- berof counterions required forneutralization, and 2. with1/20oforiginalwater (Dry2) and3/4of theoriginal counterions. The stretching profiles for A13 are presented in figure 4.13. The influence of the decreasednumber of counterions is visible here. The overstretching transition oc- 66
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Charge Transport in DNA Insights from Simulations
Titel
Charge Transport in DNA
Untertitel
Insights from Simulations
Autor
Mario Wolter
Verlag
KIT Scientific Publishing
Datum
2013
Sprache
englisch
Lizenz
CC BY-SA 3.0
ISBN
978-3-7315-0082-7
Abmessungen
17.0 x 24.0 cm
Seiten
156
Schlagwörter
Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
Kategorien
Naturwissenschaften Chemie

Inhaltsverzeichnis

  1. Zusammenfassung 1
  2. Summary 3
  3. 1 Introduction 5
  4. 2 TheoreticalBackground 11
    1. 2.1 MolecularMechanics 11
    2. 2.2 MolecularDynamicsSimulation 13
      1. 2.2.1 Solving theEquationsofMotion 14
      2. 2.2.2 ThermodynamicEnsembles 15
    3. 2.3 QuantumChemistry 18
      1. 2.3.1 DensityFunctionalTheory 18
      2. 2.3.2 ApproximativeDFT–Density-FunctionalTight-Binding 21
    4. 2.4 DynamicsofExcessCharge inDNA 24
      1. 2.4.1 TheMulti-ScaleFramework 25
      2. 2.4.2 TheFragmentOrbitalApproach 26
    5. 2.5 ChargeTransport inDNA 29
      1. 2.5.1 Landauer–BüttikerFramework 29
    6. 2.6 ChargeTransfer inDNA 32
      1. 2.6.1 Basics ofChargeTransfer 32
      2. 2.6.2 Non-adiabaticPropagationSchemes 34
  5. 3 SimulationSetup 39
    1. 3.1 TheDNAMolecule 39
      1. 3.1.1 InvestigatedDNASequences 42
    2. 3.2 MDSimulationofDNA 44
    3. 3.3 DNAunderMechanical Stress 45
    4. 3.4 MicrohydratedDNA 46
  6. 4 DNAUnderExperimentalConditions 49
    1. 4.1 FreeMDSimulations 50
    2. 4.2 TheStructuralChangesofDNAuponStretching 51
    3. 4.3 IrreversibilityofDNAStretching inSimulations 56
    4. 4.4 Effects ofLowHydration 58
    5. 4.5 Effects ofDecreased IonContent 62
    6. 4.6 Effect ofWater and Ionson theStretchingProfileofDNA 64
    7. 4.7 Conclusion 67
  7. 5 ChargeTransport inStretchedDNA 69
    1. 5.1 InvestigatedSequences andStructures 69
    2. 5.2 ChargeTransportCalculations 71
    3. 5.3 SequenceDependentChargeTransport 73
    4. 5.4 DetailedStructuralDifferences 74
    5. 5.5 Conclusion 76
  8. 6 ChargeTransport inMicrohydratedDNA 79
    1. 6.1 InvestigatedSequences andStructures 79
    2. 6.2 ChargeTransferParameters 80
    3. 6.3 ChargeTransportCalculations 84
    4. 6.4 DirectDynamicsofChargeTransfer 86
    5. 6.5 Conclusion 87
  9. 7 AParametrizedModel toSimulateCT inDNA 89
    1. 7.1 Creating theElectronicCouplings 90
    2. 7.2 Modeling the IonizationPotentials 93
    3. 7.3 TestingwithChargeTransportCalculations 97
    4. 7.4 ChargeTransferExtensions 98
    5. 7.5 TestingwithChargeTransferMethods 102
    6. 7.6 Conclusion 103
  10. 8 Conclusion 105
  11. Appendix 111
  12. A DNAUnderExperimentalConditions 111
    1. A.1 TheStructuralChangesofDNAuponStretching 111
    2. A.2 Effect ofLowHydrationandDecreased IonContent 112
    3. A.3 StretchingofMicrohydratedDNA 116
  13. B CTinMicrohydratedDNA 117
    1. B.1 HelicalParameters -CompleteOverview 117
    2. B.2 ElectronicCouplings 118
    3. B.3 IonizationPotentials 119
    4. B.4 ESP InducedbyDifferentGroupsofAtoms 122
    5. B.5 DistanceofChargedAtomGroups fromtheHelicalAxis 123
  14. List ofPublications 137
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Charge Transport in DNA